December 2017 Commit Log

Number of Commits:
127
Number of Active Developers:
10
allen 2017-12-29 16:05 Rev.: 57532

minor reformating for consistancy

0 lines of code changed in 2 files:

allen 2017-12-28 19:46 Rev.: 57531

remove shared state

0 lines of code changed in 2 files:

allen 2017-12-28 18:29 Rev.: 57530

removed the need for the grid to be passed

0 lines of code changed in 8 files:

allen 2017-12-27 19:28 Rev.: 57529

added additional state labels

0 lines of code changed in 4 files:

allen 2017-12-27 19:28 Rev.: 57528

changed overrideVariableBehavior not to copy

4 lines of code changed in 1 file:

allen 2017-12-27 19:27 Rev.: 57527

reordered checks so not duplicated

0 lines of code changed in 2 files:

allen 2017-12-27 19:24 Rev.: 57526

removed shared state call for regrider

16 lines of code changed in 13 files:

allen 2017-12-27 19:22

removed unneeded header files

0 lines of code changed in 8 files:

allen 2017-12-27 17:30 Rev.: 57523

added a print method

0 lines of code changed in 2 files:

harman 2017-12-27 12:25 Rev.: 57522

Removed space. High water memory failures will now be caught.

0 lines of code changed in 2 files:

allen 2017-12-26 15:51 Rev.: 57520

replaced the modelsetup class with a specific class for the fluids based models

292 lines of code changed in 96 files:

jthornoc 2017-12-26 11:27 Rev.: 57519

Improving the print statement at startup.

0 lines of code changed in 4 files:

ahumphrey 2017-12-22 17:53 Rev.: 57518

Make VarLabel::m_name private.

0 lines of code changed in 2 files:

allen 2017-12-22 17:15 Rev.: 57517

Removed the redundant ModelInfo class from the models to make models more generic

818 lines of code changed in 50 files:

harman 2017-12-22 11:47 Rev.: 57516

Limit the tests that are run on the gpu_RT.

0 lines of code changed in 2 files:

allen 2017-12-21 23:44 Rev.: 57514

call to acces method

0 lines of code changed in 2 files:

ahumphrey 2017-12-21 21:35 Rev.: 57513

VarLabel: DebugStream --> Dout so info is legible when output by multiple threads.
Other cleanup and refactoring.

275 lines of code changed in 5 files:

allen 2017-12-21 21:23 Rev.: 57512

added second interface computeTaskGraphIndex to remove need for shared shate call, renamed recomputeTimeStep to recomputeDelT for a more accurate call

149 lines of code changed in 55 files:

allen 2017-12-21 18:13 Rev.: 57511

added build options and renamed the script

33 lines of code changed in 2 files:

harman 2017-12-21 15:29 Rev.: 57508

Added James and Tony to the gpu_rt email list.
Now compiling all components on gpu_rt.

0 lines of code changed in 4 files:

allen 2017-12-21 14:51 Rev.: 57507

cleaned up the dependency checks and removed the double negative directives

133 lines of code changed in 11 files:

allen 2017-12-21 14:50 Rev.: 57506

standardized the error output for the factories

0 lines of code changed in 20 files:

allen 2017-12-21 14:49 Rev.: 57505

removed duplicate output

0 lines of code changed in 2 files:

allen 2017-12-21 14:49 Rev.: 57504

fixed warning and used declared var

1 lines of code changed in 1 file:

allen 2017-12-21 09:47 Rev.: 57502

added ordering warning for static builds

15 lines of code changed in 2 files:

bisaac 2017-12-21 09:14 Rev.: 57501

Added gas phase enthalpy contribution during particle destruction at the wall. No impact on regression tests.

0 lines of code changed in 4 files:

bisaac 2017-12-20 23:12 Rev.: 57500

Updated deposition velocity to be consistent with mass evolving at the wall, and fixed a bug when computing the volume-averaged particle size. This commit will break 1GW_RT and 1GW_em_tc.

0 lines of code changed in 10 files:

allen 2017-12-20 19:24 Rev.: 57499

Found more models that need dependcy checks

27 lines of code changed in 3 files:

allen 2017-12-20 19:08 Rev.: 57498

added if defs checks

95 lines of code changed in 4 files:

allen 2017-12-20 18:00 Rev.: 57497

added code to build analysis modules based on application dependency

32 lines of code changed in 5 files:

allen 2017-12-20 17:11 Rev.: 57496

Remvoed extra line

0 lines of code changed in 1 file:

allen 2017-12-20 16:59 Rev.: 57495

Changed ordering

4 lines of code changed in 1 file:

allen 2017-12-20 16:48 Rev.: 57494

Fixed typo in Makefile and added dependent libs

53 lines of code changed in 9 files:

allen 2017-12-20 15:55 Rev.: 57493

Changed ordering for static builds

2 lines of code changed in 1 file:

harman 2017-12-20 15:40 Rev.: 57491

Changes for the buildbot.

Added RayKokkos.cc to the sed commnd.

0 lines of code changed in 2 files:

allen 2017-12-20 15:25 Rev.: 57490

added comments on the models

13 lines of code changed in 2 files:

allen 2017-12-20 15:24 Rev.: 57489

added sub libs to the makefile

31 lines of code changed in 1 file:

allen 2017-12-20 13:45 Rev.: 57488

added missing header files and clean up of the class for forward declare

0 lines of code changed in 24 files:

derekhar 2017-12-20 12:53 Rev.: 57487

Add Table interface for paritcle radiation properties.

0 lines of code changed in 8 files:

allen 2017-12-20 12:19 Rev.: 57486

added missing header files and clean up of the class for forward declare

82 lines of code changed in 10 files:

allen 2017-12-20 11:06 Rev.: 57485

deprecated the ModelMaker as it is no longer a component

0 lines of code changed in 2 files:

allen 2017-12-20 11:02 Rev.: 57484

Broke the large libs into smaller libraries allowing of the removal the ModelFactory Component and moved all application code from core

97344 lines of code changed in 1019 files:

allen 2017-12-19 18:00 Rev.: 57483

removed fubar code

0 lines of code changed in 2 files:

ahumphrey 2017-12-19 15:29 Rev.: 57481

* Finish repairs and cleanup in Core/Malloc, specifically the Uintah default Allocator (when SCI_MALLOC is enabled). Remove legacy pthread code, recursive locks, etc. Use std::mutex, no need for recursive mutex.

* Remove sci_system, use std:system

* Remove all remaining pthread remnants (including THREAD_LIBRARY references). Only use and rely on std::thread. Should have never been mixing pthreads with std::thread. Can't bank on what the underlying thread impl is.

* Generate new configure script.

* Lastly, fix issue with MPM PetscSolver include. Now Uintah compiles without Petsc (e.g. --without-petsc), as it should be able to.

342 lines of code changed in 75 files:

bisaac 2017-12-19 13:04 Rev.: 57479

Added the ability to retain the organic mass after deposition. The parameter retained_deposit_factor can be used to specify the fraction of organic that remains the in the deposit.

174 lines of code changed in 6 files:

allen 2017-12-18 21:18 Rev.: 57478

Moved MPM Solvers and other class into their own sub dirs

4 lines of code changed in 5 files:

allen 2017-12-18 20:48 Rev.: 57477

Moved MPM Solvers and other class into their own sub dirs

3303 lines of code changed in 119 files:

allen 2017-12-18 19:55 Rev.: 57476

Made the models a first class component and minor clean up the MPM header file usage

851 lines of code changed in 112 files:

jholmen 2017-12-18 18:58 Rev.: 57475

* Added a template parameter to compute4Flux to manage the KokkosView3 type for intensity.

0 lines of code changed in 2 files:

derekhar 2017-12-18 18:36 Rev.: 57474

Rips out the Chemistry Table from arches so that it can be used as a standAlone object. This will be useful going forward for multiple tables, which often need different interfaces.

1450 lines of code changed in 6 files:

allen 2017-12-18 17:53 Rev.: 57473

added access to the regridder and fixed typo

6 lines of code changed in 3 files:

bpeterson 2017-12-18 16:01 Rev.: 57472

Dav and I chatted about this. Ubuntu 17 has issues when compiling this file, which we think is caused by a bug in 2.26. Our "fix" for now is just to put a comment in that file giving the user an alternative edit that will get Uintah to compile. A future fix would be an additional #ifdef check to make this automatic

1 lines of code changed in 1 file:

bpeterson 2017-12-18 15:47 Rev.: 57471

Made a goof, committed from an older version. This is a better commit without printf comments displaying.

5 lines of code changed in 1 file:

bpeterson 2017-12-18 15:45 Rev.: 57470

This fixes a race condition when a node has multiple scheduler threads processing multiple patches from MPI neighbors.

120 lines of code changed in 1 file:

allen 2017-12-18 15:04 Rev.: 57469

backer out the scheduling of the report stats and check in-situ

16 lines of code changed in 1 file:

jthornoc 2017-12-18 12:16 Rev.: 57468

Add a kokkos_translate flag to the DQMOM section so that this code is
only activated when intended.

0 lines of code changed in 2 files:

jthornoc 2017-12-18 12:16 Rev.: 57467

Adding initial implementation of DQMOM in the
Arches/Kokkos/TaskInterface mode.

This still needs some work...

523 lines of code changed in 23 files:

guilkey 2017-12-18 11:19 Rev.: 57466

Replace "length" in the cohesive zone code with "area" which is what it really
should have been called in the first place.

27 lines of code changed in 8 files:

jholmen 2017-12-17 18:32 Rev.: 57465

* Replaced use of std::vector within rayTrace_dataOnion_solveDivQFunctor with arrays of plain old data and views.
* Templated rayTrace_dataOnion_solveDivQFunctor on maxLevels.
* Added the FIXED_RANDOM_NUM macro.
* Removed use of d_isSeedRandom within functors.
* Hard-coded use of d_flowCell within functors.

202 lines of code changed in 1 file:

jholmen 2017-12-15 23:57 Rev.: 57464

* Setup views outside of functors.
* Updates to work with more plain old data within functors.

122 lines of code changed in 1 file:

jholmen 2017-12-15 16:50 Rev.: 57461

* Added RayKokkos.h.
* Replaced use of MersenneTwister with KokkosRandom.
* Removed rayDirection_cellFace.
* Removed rayDirectionHyperCube_cellFace.
* Removed findRayDirectionHyperCube.
* Removed rayLocation_cellFace.

This commit replaces use of the MersenneTwister with a portable Kokkos alternative. This alternative is based on Vigna, Sebastiano (2014). "An experimental exploration of Marsaglia's xorshift generators, scrambled." http://arxiv.org/abs/1402.6246

Note, this generator is seeded using the time. To enable comparisons with Ray:CPU, define FIXED_RANDOM_NUM in src/Core/Math/MersenneTwister.h. To enable comparisons with Ray:GPU, define FIXED_RANDOM_NUM in src/CCA/Components/Models/Radiation/RMCRT/RayGPUKernel.cu.

This commit also removes functions featuring use of the MersenneTwister. These have been (or will be) brought into functors.

512 lines of code changed in 2 files:

ahumphrey 2017-12-15 15:16 Rev.: 57459

Define scinew to new when defined( DISABLE_SCI_MALLOC )

6 lines of code changed in 1 file:

allen 2017-12-15 14:58 Rev.: 57458

fixed typos fro PIDX

1 lines of code changed in 1 file:

ahumphrey 2017-12-15 14:35 Rev.: 57457

Beginnings MALLOC_TRACE support removal, e.g. MALLOC_TRACE_TAG_SCOPE and other macros.

This library, though once useful, no longer works with Uintah and is not maintained, plus inextricably tied to SCI_MALLOC, which ultimately needs to go away.

94 lines of code changed in 24 files:

ahumphrey 2017-12-15 12:33 Rev.: 57456

Additional Uintah::Allocator cleanup.

130 lines of code changed in 2 files:

jholmen 2017-12-14 23:03 Rev.: 57455

* Removed updateSumI_ML.
* Removed boundary flux calculations.

updateSumI_ML functionality has been brought into rayTrace_dataOnion_solveDivQFunctor.

Boundary flux calculations have been temporarily removed in preparation for replacing the MersenneTwister with a portable Kokkos alternative.

11 lines of code changed in 1 file:

jholmen 2017-12-14 20:29 Rev.: 57454

* Updated multi-level RMCRT:Kokkos to match the implementation within Ray.cc r57329.

581 lines of code changed in 1 file:

allen 2017-12-14 19:42 Rev.: 57453

renamed ComponentFactory to Applicationfactory - moved model mgt from switcher to application

482 lines of code changed in 14 files:

harman 2017-12-14 19:07 Rev.: 57452

Redefined NIGHTLYTEST so the buildbot:gpu will execute gpu kernel tests.

0 lines of code changed in 2 files:

jholmen 2017-12-14 18:52 Rev.: 57451

* Updated to std::ostringstream for Hypre-less builds.

3 lines of code changed in 1 file:

allen 2017-12-14 16:28 Rev.: 57450

minroclean up for readablity and removing MPM check

16 lines of code changed in 2 files:

allen 2017-12-14 16:26 Rev.: 57449

minor interface clean up and have it report the solver created in the factory

20 lines of code changed in 3 files:

allen 2017-12-14 16:23 Rev.: 57448

added a check for models and comment cleanup

18 lines of code changed in 1 file:

allen 2017-12-14 16:21

Added a name method

17 lines of code changed in 6 files:

allen 2017-12-13 19:07 Rev.: 57442

fixed Todd's booboo

0 lines of code changed in 2 files:

allen 2017-12-13 18:24 Rev.: 57441

reverting buidbot test

4 lines of code changed in 1 file:

allen 2017-12-13 18:22 Rev.: 57440

added a SolverCommon class, made OnTheFlyAnalysis a first class UintahParallelComponent, added acess methods for component controll in UintahParallelComponent

890 lines of code changed in 156 files:

harman 2017-12-13 16:57 Rev.: 57439

*.py: added usage comments

UCF.py: Added postProcessUda regression test.

runSusTests.py: Modified so postProcessUda tests will run.

52 lines of code changed in 17 files:

bpeterson 2017-12-13 16:20 Rev.: 57438

This should fix the build bot bugs preventing RMCRT_ML_GPU and RMCRT_bm1_DO_GPU. Long story short, the UnifiedScheduler was requesting all levels from all patches in the patchset, and I only needed to get the level for the active patch being computed against.

24 lines of code changed in 1 file:

jholmen 2017-12-13 13:42 Rev.: 57437

* Updated single-level RMCRT:Kokkos to match the implementation within Ray.cc r57329.

351 lines of code changed in 1 file:

harman 2017-12-13 12:52 Rev.: 57436

Global:
changed global variable names to be more descriptive.

Add proc0patch0cout() class which prints message on proc 0, patch 0 and
only n times per timesteps.

bug fixes to populate the old_dw with variables from user specified timestep

0 lines of code changed in 14 files:

allen 2017-12-13 09:41 Rev.: 57435

fixed a couple of rename vars

5 lines of code changed in 2 files:

allen 2017-12-12 20:26

Cleanup of the Scheduler to use ports for all components

739 lines of code changed in 115 files:

ahumphrey 2017-12-12 17:27 Rev.: 57432

Fix redundant calls to shutdown within Uintah::Allocator. When SCI_MALLOC was enabled, this was being called for all allocs, frees, etc, rewinding the file pointer and rewriting the stats_out file in some cases on the order of millions of times, appending redundnat info. The failing multibox_coal_rmcrt tests were not actually failing, but simply taking too long (because of this issue) and was killed because a max run time was exceeded.

Now we explicitly register shutdown function with std::atexit. This way the malloc_stats file, with accumulated data gets written once at very end. This is orders of magnitude faster than before and captures the full range of allocs, frees, occuring during entire simulation. I am convinced the previous code omitted ~5% of the total memory-related calls.

Removed USE_LENNY_HACK and LINUX_GETENV_HACK macros, and cleaned up Allocator significantly. It is now fairly readable. Need to purge MallocTrace remnants in the near future. This is additional confusing logic (interleaved with MALLOC_STATS code) for a library that no longer works with Uintah.

954 lines of code changed in 5 files:

harman 2017-12-12 14:17 Rev.: 57431

driver:
Execute chgrp on the same line as the tar |ssh command. No need to login again and execute it.

pscp2:
- Added silent_ssh function, which eliminates all the chatter from MOTD and Module load to stderr/stdout.
Ash is plagued with this! The function executes the command in a non-interactive session and
returns command output.
- Replaced $SSH calls with silent_ssh()
- redirect scp output to /dev/null
- improved bulletproofing

0 lines of code changed in 4 files:

allen 2017-12-12 14:13 Rev.: 57430

made the ApplicationInterface purely virtual and cleaned up naming

418 lines of code changed in 14 files:

jthornoc 2017-12-12 12:35 Rev.: 57429

* Remove a double delete on a source label (zzNox) - not sure why this wasn’t picked up earlier.
* Adding mass flow rt check in intrusion_test.ups. THIS CHANGES ANSWERS.
* Added some additional error checking, comments, etc. for the intrusion inlets.
* Updated a couple input files with correct uda names.

75 lines of code changed in 4 files:

ahumphrey 2017-12-11 19:09 Rev.: 57428

Fix failing multibox_rmcrt_coal tests.

Faulty logic in the use of USE_LENNY_HACK macro was causing shutdown() to be called an inordinate amounts of times, consequently having to unnecessarily rifle through all the MALLOC_STATS bookkeeping each time.

Please someone tell me that Uintah no longer needs things like USE_LENNY_HACK and LINUX_GETENV_HACK.....

7 lines of code changed in 3 files:

allen 2017-12-11 18:25 Rev.: 57427

added app tot eh load balancer

2 lines of code changed in 1 file:

allen 2017-12-11 18:25 Rev.: 57426

more cleanup of the recompiling

213 lines of code changed in 24 files:

jthornoc 2017-12-11 17:54 Rev.: 57425

Cleanup debug flag.

3 lines of code changed in 3 files:

jthornoc 2017-12-11 17:49 Rev.: 57424

Removing defunct tag and moving a SCI_DEBUG print statement.

3 lines of code changed in 1 file:

jthornoc 2017-12-11 16:25 Rev.: 57423

Move calls to scalar intrusion information after actually checking if it
exists.

9 lines of code changed in 1 file:

jthornoc 2017-12-11 16:25 Rev.: 57422

Allow the case to restart when turning on the wall model after the fact.

0 lines of code changed in 2 files:

allen 2017-12-11 15:56 Rev.: 57421

merged the needCompile into the ApplicationCommon class, removed the passing of appliction values in the DataArchiver

543 lines of code changed in 21 files:

allen 2017-12-11 15:10 Rev.: 57420

removed debug changes

3 lines of code changed in 1 file:

tsaad 2017-12-11 12:36 Rev.: 57419

Revert Mike's revert. Code was good. We had a bug in the input file. This will break Wasatch RT - so don't freak out.

33 lines of code changed in 2 files:

allen 2017-12-11 11:56 Rev.: 57418

added IntVector for particles

19 lines of code changed in 1 file:

allen 2017-12-11 10:55 Rev.: 57417

updating naming

0 lines of code changed in 2 files:

allen 2017-12-11 10:46 Rev.: 57416

fixed method name call and warning

4 lines of code changed in 1 file:

guilkey 2017-12-11 10:45 Rev.: 57415

Add ability to compare ParticleVariable<IntVector>

0 lines of code changed in 2 files:

allen 2017-12-08 19:10 Rev.: 57414

Moved PIDX checks out of the SimCtrl. Cleanup of varnames

1088 lines of code changed in 20 files:

jthornoc 2017-12-08 17:57 Rev.: 57413

Warning.

0 lines of code changed in 1 file:

jthornoc 2017-12-08 17:57 Rev.: 57412

Fix warning.

0 lines of code changed in 1 file:

jthornoc 2017-12-08 17:57 Rev.: 57411

This fixes a bug in the intrusion inlet by not setting zero valued
tangential velocity components.

Also simplify the constant (flat) velocity spec a little.

33 lines of code changed in 2 files:

jthornoc 2017-12-08 17:57 Rev.: 57410

More work on bringing the intrusion inlets up to speed.
Handoff capability seems to be working. Still needs verification.
Added some input files for demo purposes.
RT test to come later after verification.

409 lines of code changed in 12 files:

jthornoc 2017-12-08 17:57 Rev.: 57409

Updating the scalar handoff stuff. Starting the velocities.

80 lines of code changed in 4 files:

jthornoc 2017-12-08 17:57 Rev.: 57408

Adding a helper class for dealing with handoff files.

126 lines of code changed in 4 files:

guilkey 2017-12-08 17:45 Rev.: 57407

Dumb things down a bit so that the switchEx3 test will pass. Basically, the arches
heat flux won't support multiple load curves per particle like the other PhysicalBCs.

6 lines of code changed in 1 file:

guilkey 2017-12-08 15:12 Rev.: 57406

Removed commented out code from AMRMPM, fixed some more overlooked pLoadCurveID
in ImpMPM.

21 lines of code changed in 2 files:

allen 2017-12-08 11:33 Rev.: 57405

made the reporting of stat and the the in-situ a task

24 lines of code changed in 2 files:

guilkey 2017-12-07 13:27 Rev.: 57403

Switch the load curve data type to IntVector as has already been done in the explicit
code.

18 lines of code changed in 1 file:

guilkey 2017-12-06 18:06 Rev.: 57401

Particles can now be part of up to three load curves. This is particularly
useful for pressure BCs where pressure might be applied to more than one
face, now corner particles get contributions from both, with the resultant force
as the sum of the two forces from each face's load curve. This will break the
NairnFriction test in the RT.

147 lines of code changed in 22 files:

harman 2017-12-06 15:36 Rev.: 57400

Added infrastructure so a module(s) can fill the old_dw with a timestep from the uda.

spatioTemporalAvg:
Added temporal avg calculation. Not fully working.

139 lines of code changed in 9 files:

harman 2017-12-05 18:05 Rev.: 57399

Module.*
CreateMatlSet() - cleaned out confusing code
readTimeStartStop() - put udaTimesteps into a global var.

PostProcess.*
remove unused methods
problemSetup() - set the simulation state time and removed hack.
computeDelT() - fixed calculation on last timestep.

38 lines of code changed in 4 files:

allen 2017-12-05 16:24 Rev.: 57398

commented out test line and added comments

4 lines of code changed in 2 files:

allen 2017-12-05 15:10 Rev.: 57397

changed the stored delta T to actual delta T used for the next time step

463 lines of code changed in 7 files:

allen 2017-12-05 15:09 Rev.: 57396

changed/removed PostProcessUda calls

2 lines of code changed in 1 file:

allen 2017-12-05 15:09 Rev.: 57395

moved specific calls to apllication form Sus and SimCtrl

13 lines of code changed in 1 file:

derekhar 2017-12-04 16:28 Rev.: 57393

Added bullet proofing for DORadiation sweeps when used with staggered patch layouts. Collapsed code that had been copied and pasted into for loop.

0 lines of code changed in 4 files:

harman 2017-12-04 11:58 Rev.: 57392

gpu_rt configure line:

--enable-gencode=35 -> 52

1 lines of code changed in 1 file:

harman 2017-12-04 11:41 Rev.: 57391

Write tmp files to /tmp/ allowing a non-owner to copy the uda.

5 lines of code changed in 1 file:

ahumphrey 2017-12-03 16:12 Rev.: 57389

Eliminate copy, assignment and move.
Remove using namespace std.
Remove unused include.

89 lines of code changed in 4 files:

ahumphrey 2017-12-01 18:22 Rev.: 57385

Transition from DebugStream to Dout within SimulationController for debug reporting. Signifcant other cleanup and formatting.

836 lines of code changed in 4 files:

harman 2017-12-01 16:50 Rev.: 57384

added reduce_uda option, which just avoids creating any modules.

sched_readDataArchive()
- Simplified the code to create the material set for each VarLabel and all VarLabels.


34 lines of code changed in 3 files:

ahumphrey 2017-12-01 15:57 Rev.: 57383

Fix shadowing issue on problemSetup() for several scheduler implementations.

25 lines of code changed in 9 files:

allen 2017-12-01 11:26 Rev.: 57382

updates to the output messages

24 lines of code changed in 1 file:

November 2017 »

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